1. Field of the Invention
The present invention relates to optical imaging. More particularly, the present invention relates to reading out spectral data from an optical sensor. Still more particularly, the present invention relates to an apparatus, method and software program product for enhancing the dynamic range of spectral data read from an imaging sensor.
2. Description of Related Art
The present invention relates to optical spectroscopy measurement instruments which employ an array of sensors in the focal plane to provide substantially simultaneous measurement of light intensity at multiple wavelengths over a broad wavelength range. The advantage of being able to monitor many wavelengths at once has led to the proliferation of these instruments, known collectively as spectrographs. Prior to the development of solid state sensor arrays, the spectroscopy instrument of choice was the monochromator. In a monochromator, a single narrow wavelength region is selected for measurement, and a single detector is used. The ability to make simultaneous independent measurements at different wavelengths is a significant advantage in many applications. Nevertheless, performance limitations of available detector arrays often prevent the use of spectrographs in some demanding applications. One important limitation is dynamic range. It is a general property of solid state sensor arrays that they can only simultaneously measure signals whose magnitude lies within a specific range known as the dynamic range. It is this limitation that is addressed by this invention.
A spectrograph in the prior art consists of an optical imaging system, a light detecting system, and a data processing element. The optical imaging system analyzes light into its component spectral features. The analyzed light is converted to an electrical signal by the light detecting system, and the electrical signal is converted to a numerical or graphical representation of the light's intensity as a function of wavelength and time by the data processing element.
A good detailed description of the optical imaging component of a spectrograph is “The Optics of Spectroscopy: a Tutorial,” by J. M. Lerner and A. Thevenon, which is incorporated herein by reference in its entirety. It is available on the World Wide Web at the site of the Jobin Yvon Horiba company at jvhoriba.co.uk/jy/oos/oosl. In a typical spectrograph, light enters through a slit and is dispersed by a grating or prism by an angle dependent on the wavelength. The slit is imaged in the focal plane, and the image can be visualized as a rectangle with the long dimension which corresponds to wavelength determined by the dispersion (FIG. 1). The useful wavelength range of the spectrograph consists of a continuous distribution in wavelength between short and long wavelength limits λ1 and λn. The other dimension is determined by the slit length, the imaging characteristics of the optics, and the required performance, since in practice, the wavelength separation is usually best in the middle and degrades as one goes towards the edges.
The light detection system in a spectrograph is a detector array placed in the focal plane which allows readout of the spectral information. In order to have good spectral resolution, it is desirable that the individual sensor elements (pixels) be small in the wavelength dimension. A typical dimension is on the order of 10 micrometers. In the other dimension, it is usually desirable to have each pixel be as large as possible, up to the useable dimension of the image, in order to have a good signal-to-noise ratio. For spectrographs used in the ultraviolet to near-infrared range (about 190 nm to 1100 nm), photodiode arrays (PDAs), charge-coupled devices (CCDs) and charge injection devices (CIDs) are commonly used detectors.
PDAs are linear arrays of square or rectangular sensors. In this application, the sensors are distributed along the wavelength axis of the image. In that direction, a typical dimension is on the order of 10 micrometers. In the other direction, the pixels may be as long as several hundred microns or longer. An example of a PDA designed for spectroscopy is the RL1210LGQ-711 made by Perkin Elmer Optoelectronics, Inc., 2175 Mission College Boulevard, Santa Clara, Calif. 95054; Telephone: (408) 565-0850) which has a total light sensing area of 2.5 mm by 25.6 mm. It is divided into 1024 sensor elements each with dimensions of 25 microns by 2500 microns. The rectangular pixels are suited to the simultaneous requirements of being small along the wavelength axis and large along the slit direction.
For demanding applications, however, CCDs are often preferred over PDAs, since in CCDs the inherent electrical noise can be made much lower. A detailed description of a modern CCD used for spectroscopy can be found in the document “An Introduction to Scientific Imaging Charge-Coupled Devices” published by Scientific Imaging Technologies, Incorporated, which is incorporated herein by reference in its entirety and available on the World Wide Web at autovision.net/CCDs.pdf or site-inc.com/pdf/introdat.pdf. An example of such a CCD is the S7031-1007 device manufactured by the Hamamatsu Corporation of Japan (HAMAMATSU PHOTONICS K.K., Solid State Division; 1126-1 Ichino-cho, Hamamatsu City, 435-8558 Japan, Telephone: (81) 053-434-3311, Fax: (81) 053-434-5184, http://www.hamamatsu.com; U.S.A.: Hamamatsu Corporation: 360 Foothill Road, P.O. Box 6910, Bridgewater, N.J. 08807-0910, U.S.A., Telephone: (908) 231-0960. The total light sensing area of this device is 25.6 mm by 3.1 mm The total sensing area is nearly the same as that of the PDA referenced above, but, as is typical of CCDs, the individual pixels are small and square (24 microns on a side) and arranged in a two-dimensional array.
FIG. 2 is a diagram which generally depicts the functional elements of a typical CCD sensor including array 200 which is configured as a square (or rectangular) N×M array of pixels 202 having N lines of M pixels each, configured in a parallel shifting architecture, serial shift register 206 comprised of a plurality of individual shift registers, summing well 210 and amplifier 212. As shown in the diagram, array 200 is generally configured as N parallel lines of M pixels each. Each pixel is each coupled to another for transporting charges vertically down the columns, from row to row, in parallel to individual shift registers 206-1 through 206-N of serial shift register of serial register 206. Each of pixels 202 transfers charge vertically in only one direction. The last row of the array is serial (or horizontal) shift register architecture 206 which transfers charge in an orthogonal direction to that of the parallel architecture using shift registers 206-1 through 206-N using the same coupling between registers. Every pixel may be read individually, or the charge from groups of pixels may be read together in various ways.
As well understood by those of ordinary skill in the art, a CCD operationally converts light photons to charge in any pixel being struck by the photon and the charge is then held in the pixel well until readout. An individual pixel well holds a finite amount of charge, which is defined as its full well capacity, above which the well becomes saturated. The period of time that the CCD sensor is exposed to light and charge is allowed to accumulate in the pixel wells is referred to as the “integration time.” After the integration time has elapsed, the array is read. In the case where the signal from each pixel is to be read individually, array readout commences by the simultaneous clocking all rows of charges one pixel toward horizontal shift registers 206-1 through 206-N. The charges are shifted between pixels 202 by means of the parallel shift architecture from one horizontal row of pixels to the next horizontal row from top to bottom of pixel array 200. The bottom row of charge is transferred into the linear array of shift registers 206-1 through 206-N. Serial shift register architecture 206 then serially transfers the charge out of the sensor, making room for the next row to be shifted down, and the next, and so on. The resulting stream is a pixel-by-pixel, row-by-row representation of the photons striking the CCD sensor. However, prior to being transferred serially off-chip, each pixel's charge is amplified by amplifier 212, resulting in an analog output signal of varying voltage which is proportional to the pixel charge. Located between amplifier 212 and last serial shift register 210-N is summing well 210, which is used for pixel binning operations.
In an effort to further reduce electrical noise and improve the signal-to-noise ratio, albeit at the expense of reduced spatial resolution, the array can be read by a process known as “pixel binning.” Pixel binning is generally understood by those of ordinary skill in the art as a clocking scheme used to combine the charge collected by adjacent CCD pixels. Binning the charge from blocks of adjacent pixels reduces noise by creating a larger sample area on the CCD. Binning is typically performed in either “area binning mode” or “line binning mode.” In area binning mode charge from a square or rectangular array of pixels is combined into a super-cell value by the sensor and then output for further processing, e.g., 2×2 binning combines the charges from a block of four pixels into a single output signal; 3×3 binning combines the charge from nine pixels and so on.
The 2×2 binning process involves two consecutive vertical shifts into the serial shift register, and a series of horizontal shifts, two at a time, into the summing well. Operationally, following the integration period, the charge from the two horizontal pixel rows closest to the horizontal shift registers are read in parallel readout and shifted into their respective horizontal shift registers, thereby aggregating two pixel's charges into a single horizontal shift register. The charge from every other pixel in each line is also transferred two pixels closer to the horizontal shift registers. After two vertical shifts, two consecutive horizontal shifts move the charge from two end registers into the summing well. The summing well then holds a cumulative charge from the 2×2 block of pixels, which is then amplified and converted to a voltage for further off-chip amplification and digitization. Charge from any number of pixels can be shifted into a shift register, but once the well of the shift register is saturated, any additional charge shifted from the pixels is disregarded. If any charge is not retained in a horizontal shift register, the intensity for the binned pixel is incorrect, i.e., reduced by the amount of the charge not retained in the line shift register. In spectroscopy applications, line binning mode is typically used for readout. FIG. 3 is a diagram depicting the spectral image of FIG. 1 superimposed over the sensing portion of the pixel array of a CCD sensor as depicted in FIG. 2. Notice from the diagram that the spectra wavelengths correspond to the vertical lines of pixels in array 200. Since the individual pixels are small, the signal from many pixels corresponding to the same wavelength are typically binned to effectively create a single rectangular sensor for each wavelength. By using this correspondence, the level of noise can be reduced and the signal-to-noise ratio is improved by binning the pixels corresponding to the spectra wavelengths into a single super-cell. This is done by reading the CCD in line binning mode.
FIG. 4 is a flowchart depicting a process for reading out an N×M pixel array CCD sensor in line binning mode according to the prior art. The binning process begins after each integration by vertically reading out the pixel signals of each line. Charge is shifted down the N vertical shift registers, in parallel row-by-row fashion, to the N horizontal shift registers (step 402). Vertical shifting accumulates the charge of each pixel line into the last shift register of the column, which is actually a horizontal shift register in the serial shift register. Next, the charge from each of the N pixel lines is shifted out of the N horizontal shift registers, column-by-column, in N horizontal shifts (step 404). Rather than summing these charges in a summing well, the line pixel data is output off the chip in a column-by-column fashion (step 406). The result of reading the CCD is an analog signal whose amplitude varies with time. The analog signal is then amplified, converted into a digital form, whereupon the necessary calculations are performed so that the data can be represented, e.g., as a table of light intensity vs. wavelength. Typically, the intensity values are presented as integer values within some convenient range, as, for example, 0-65535 in the case where a 16-bit digitizer is used.
The dynamic range of a CCD is related to the ratio of well depth to the readout noise, usually expressed in decibels. The limitation to dynamic range in a CCD-based spectrograph exists because there is a limit to the amount of charge that each pixel and each horizontal shift register can hold. Inaccurate measurements result if the charge accumulated in any pixel, or any shift register, reaches this saturation level. By contrast, several noise sources exist in the readout process which cause inherent uncertainty in the measurement of the charge in any shift register. Therefore, the useful range of a measurement is when the charge is between the inherent noise level and below the full-well, or saturation level. A typical dynamic range specification for a scientific-grade CCD intended for spectroscopy is 75000.
As alluded to above, the amount of charge which accumulates in a column of pixels of a spectroscopy CCD array is proportional to both the light intensity at the wavelength which illuminates that column and the amount of time that charge is allowed to accumulate before it is read. Again, that time is defined as the integration time. The integration time has to be chosen so that the quantity of charge in each column lies within the useful range. A problem occurs if the spectrum of interest includes regions of widely differing intensity, since there may be no single integration time which is suitable for the entire spectrum. Furthermore, for spectra including extremely bright features, it may not be possible to use an integration time short enough to prevent saturation of the brightest lines, since the minimum achievable integration time is the time it takes to perform one full vertical and one full horizontal shift.
The dynamic range limitation has been dealt with in many different ways, some of which are mentioned here. One way is to interleave spectral acquisitions using different integration times. A single composite spectrum with high dynamic range can be derived from individual spectra acquired using different integration times. However, this approach does not solve the problem of lines which are saturated at the shortest integration time. Another approach, described by Brooks (U.S. Pat. No. 5,675,411) which is incorporated herein by reference in its entirety, is to incorporate a photomask into the spectrometer to selectively attenuate bright lines. However, this approach is not applicable if the spectrograph is to be used to analyze diverse sources. Yet another approach is to modify the design of the sensor to improve the dynamic range. One example of this is the sensor described by Yadid-Pecht, et al. in U.S. Pat. No. 6,175,383, which is also incorporated herein by reference in its entirety. Yadid-Pecht et al. teach incorporating circuitry that allows the integration time on each pixel to be individually set. Considerations of cost and manufacturability, however, make it desirable to have an alternative approach which is applicable to existing high-performance CCDs of moderate cost.
Other features of the present invention will be apparent from the accompanying drawings and from the following detailed description.